Commits · 165c67ccdabfaf1de1fba004a06c4ab8b9928a6f · OpenDAS / dgl

24 May, 2020 1 commit

[DGL-LifeSci] Pre-trained GIN (#1558) · 165c67cc

Mufei Li authored May 25, 2020

* Update

* Fix

* Update

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165c67cc

16 May, 2020 1 commit

[DGL-LifeSci] WLN for Reaction Prediction (#1530) · 039fefc2

Mufei Li authored May 16, 2020

* Update

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* Fix bug

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* Finalize

039fefc2

15 Apr, 2020 1 commit
- Update (#1447) · ad222fb9
  Mufei Li authored Apr 16, 2020
  
  ad222fb9
14 Apr, 2020 1 commit

[DGL-LifeSci] Weave for Molecular Property Prediction (#1441) · 011656fd

jjhu94 authored Apr 15, 2020



* featurize for weave model

* weave module for molecular graphs

* Update

* completed weave model

* update the whole weave model

* Update

* update atom (node) features

'

* "featurizer"

* Add files via upload

add edge featurizer

* Add files via upload

* Update

* Update

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Co-authored-by: mufeili <mufeili1996@gmail.com>

011656fd

09 Apr, 2020 1 commit

deprecate DGL-KE. (#1432) · e317f715

Da Zheng authored Apr 09, 2020



* deprecate DGL-KE.

* Update README.md

* remove from CI.

* remove tests.
Co-authored-by: Zheng <dzzhen@3c22fb0ed81b.ant.amazon.com>

e317f715

02 Apr, 2020 2 commits
- [DGL-LifeSci] Documentation (#1414) · d3560b71
  Mufei Li authored Apr 02, 2020
```
* Update

* Update

* Update
```
  d3560b71
- [DGL-LifeSci] Final release preparation for 0.2.1 · 0ee9f56e
  Mufei Li authored Apr 02, 2020
  
  0ee9f56e
01 Apr, 2020 1 commit

[DGL-LifeSci] Release Preparation (CI, Docker, Conda build) (#1399) · b76ac11c

Mufei Li authored Apr 01, 2020



* Update

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* add docs

* Fix style

* Fix lint

* Bug fix

* Fix test

* Update

* Update

* Update

* Update
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

b76ac11c

19 Mar, 2020 1 commit

[KG]Update README and config (#1375) · 1b9bc16b

xiang song(charlie.song) authored Mar 19, 2020



* Update README and config

* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-60-78.ec2.internal>

1b9bc16b

17 Mar, 2020 2 commits

[DGL-KE] Add license to every file header (#1368) · 635dfb4a

Chao Ma authored Mar 17, 2020

* update metis

* update

* update dataloader

* update dataloader

* new script

* update

* update

* update

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* update

* update dataloader

* update

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* Add license to every filer header

635dfb4a

[DGL-KE] Add METIS preprocessing pipeline (#1365) · f8ae6350

Chao Ma authored Mar 17, 2020

* update metis

* update

* update dataloader

* update dataloader

* new script

* update

* update

* update

* update

* update

* update

* update

* update dataloader

* update

* update

* update

* update

* update

f8ae6350

16 Mar, 2020 1 commit
- Update (#1366) · 2ce0e21b
  Mufei Li authored Mar 16, 2020
  
  2ce0e21b
15 Mar, 2020 2 commits

fix. (#1358) · f9ad1c80
Da Zheng authored Mar 14, 2020
```
Co-authored-by: Chao Ma <mctt90@gmail.com>
```
f9ad1c80

[KG] partition a KG. (#1351) · eb71c804

Da Zheng authored Mar 14, 2020



* partition a KG.

* get tid.

* support builtin

* fix a minor bug.
Co-authored-by: Chao Ma <mctt90@gmail.com>

eb71c804

14 Mar, 2020 1 commit

[DGL-LifeSci] WLN for Reaction Center Prediction (#1360) · 545cc065

Mufei Li authored Mar 14, 2020

* Update

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545cc065

13 Mar, 2020 1 commit
- Update (#1359) · f3b866f4
  Mufei Li authored Mar 13, 2020
  
  f3b866f4
12 Mar, 2020 1 commit
- Fix for dataloader (#1353) · 87842db4
  xiang song(charlie.song) authored Mar 12, 2020
  
  87842db4
11 Mar, 2020 1 commit
- fix sampler. (#1350) · 9432cd63
  Da Zheng authored Mar 10, 2020
  
  9432cd63
10 Mar, 2020 1 commit
- [KG] make batch size compatible with neg sample size (#1343) · e6584043
  Da Zheng authored Mar 10, 2020
```
* adjust batch size.

* fix for eval.py

* adjust parameters in distributed training.

* move code.
```
  e6584043
09 Mar, 2020 3 commits

[DGL-KE] Clean up argument for DGL-KE (#1325) · d98c71ef

Chao Ma authored Mar 09, 2020

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* clean up args

* change args for eval

* update

* update

* update

* update num_worker=8

* add num_proc=1

* update

* update

* add eval percent

* update

* update

* update

* save emb

* update

* update

* update

* update

* update

* remove neg_chunk_size

* update

* update

* update

* remove

* update

* remove

* change num_thread

d98c71ef

[KGE] Kg loader (#1300) · f9ba3cdc

xiang song(charlie.song) authored Mar 09, 2020



* Now dataset accepts user define datasets

* UPdate README

* Fix eval

* Fix

* Fix Freebase

* Fix

* Fix

* upd

* upd

* Update README

* Update some docstrings.

* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-8-26.us-east-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-78.us-east-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-60-78.ec2.internal>

f9ba3cdc

[KG] save config when saving the model (#1336) · 614acf2c
Da Zheng authored Mar 08, 2020
```
* save config.

* save more.
```
614acf2c

05 Mar, 2020 1 commit

[Refactor] Unify DGLGraph, BatchedDGLGraph and DGLSubGraph (#1216) · 93ac29ce

Zihao Ye authored Mar 05, 2020



* upd

* upd

* upd

* lint

* fix

* fix test

* fix

* fix

* upd

* upd

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* upd tutorial

* upd

* upd

* fix kg

* upd doc organization

* refresh test

* upd

* refactor doc

* fix lint
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu>

93ac29ce

04 Mar, 2020 1 commit
- fix s3 link (#1310) · c23a61bd
  Jinjing Zhou authored Mar 04, 2020
  
  c23a61bd
02 Mar, 2020 1 commit

[DGL-KE] Distributed training of DGL-KE (#1290) · 00ba4094

Chao Ma authored Mar 02, 2020

* update

* change name

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* change worker number

* update

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* test

* update

* update

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* remove barrier

* max_step

* update

* add complex

* update

* chmod +x

* update

* update

* random partition

* random partition

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* change num_test_proc

* update num_thread

* update

00ba4094

18 Feb, 2020 1 commit
- Update setup.py (#1270) · 97e79265
  Mufei Li authored Feb 18, 2020
  
  97e79265
16 Feb, 2020 1 commit

[KG][Optimization] Soft relation partition (#1252) · 49fe5b3c

xiang song(charlie.song) authored Feb 16, 2020

* Several optimizations on DGL-KG:
1. Sorted positive edges for sampling which can reduce random
   memory access during positive sampling
2. Asynchronous node embedding update
3. Balanced Relation Partition that gives balanced number of
   edges in each partition. When there is no cross partition
   relation, relation embedding can be pin into GPU memory
4. tunable neg_sample_size instead of fixed neg_sample_size

* Fix test

* Fix test and eval.py

* Now TransR is OK

* Fix single GPU with mix_cpu_gpu

* Add app tests

* Fix test script

* fix mxnet

* Fix sample

* Add docstrings

* Fix

* Default value for num_workers

* Add soft relation part

* Upd

* Some fix

* upd

* Now work

* Fix TransR

* Fix eval and add some doc string

* triger

* upd

* Add some training scripts for freebase multi-gpu

* upd

* upd

* upd

49fe5b3c

09 Feb, 2020 1 commit

[Optimization][KG] Several optimizations on DGL-KG (#1233) · ffe58983

xiang song(charlie.song) authored Feb 10, 2020

* Several optimizations on DGL-KG:
1. Sorted positive edges for sampling which can reduce random
   memory access during positive sampling
2. Asynchronous node embedding update
3. Balanced Relation Partition that gives balanced number of
   edges in each partition. When there is no cross partition
   relation, relation embedding can be pin into GPU memory
4. tunable neg_sample_size instead of fixed neg_sample_size

* Fix test

* Fix test and eval.py

* Now TransR is OK

* Fix single GPU with mix_cpu_gpu

* Add app tests

* Fix test script

* fix mxnet

* Fix sample

* Add docstrings

* Fix

* Default value for num_workers

* Upd

* upd

ffe58983

08 Feb, 2020 1 commit
- [DGL-LifeSci] Fix broken links (#1248) · 3f0c1005
  Mufei Li authored Feb 08, 2020
```
* Fix

* Update
```
  3f0c1005
03 Feb, 2020 1 commit

[DGL-LifeSci] Migration and Refactor (#1226) · 828a5e5b

Mufei Li authored Feb 04, 2020

* First commit

* Update

* Update splitters

* Update

* Update

* Update

* Update

* Update

* Update

* Migrate ACNN

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Finish classification

* Update

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Update

* Update

* trigger CI

* Fix CI

* Update

* Update

* Update

* Add default values

* Rename

* Update deprecation message

828a5e5b

10 Jan, 2020 1 commit
- [KG][Optimization] Remove copy from parent in minibatch generation (#1193) · cd9599ab
  xiang song(charlie.song) authored Jan 11, 2020
```
* remote copy from parent

* upd

* make test_sampler easier to pass
```
  cd9599ab
08 Jan, 2020 1 commit

[Feature][KG] Multi-GPU training support for DGL KGE (#1178) · bb6a6476

xiang song(charlie.song) authored Jan 08, 2020

* multi-gpu

* Pytorch can run but test has acc problem

* pytorch train/eval can run in multi-gpu

* Fix eval

* Fix

* Fix mxnet

* trigger

* triger

* Fix mxnet score_func

* Fix

* check

* FIx default arg

* Fix train_mxnet mix_cpu_gpu

* Make relation mix_cpu_gpu

* delete some dead code

* some opt for update

* Fix cpu grad update

bb6a6476

05 Jan, 2020 1 commit

[KG] PBG's way of constructing negative edges (#1159) · 1022d5d6

Da Zheng authored Jan 04, 2020

* attach positive.

* add neg_deg_sample.

* add comment.

* add neg_deg_sample for eval.

* change the edge sampler.

* rename edge sampler in KG.

* allow specifying chunk size and negative sample size separately.

* fix bugs in KG.

* add check in sampler.

* add more checks.

* fix

* add comment.

* add comments.

1022d5d6

04 Jan, 2020 1 commit

[KG] More fixes on eval (#1168) · 1de192f4

Da Zheng authored Jan 04, 2020

* remove parallel sampling for multiprocessing.

* avoid memory copy in eval.

* remove print.

1de192f4

03 Jan, 2020 1 commit
- [KG] Disable filter in evaluation (#1162) · 346bc235
  Da Zheng authored Jan 02, 2020
```
* add no_eval_filter

* fix eval.
```
  346bc235
02 Jan, 2020 1 commit
- merge eval results in all processes. (#1160) · 7451bb2a
  Da Zheng authored Jan 01, 2020
  
  7451bb2a
31 Dec, 2019 1 commit

Accelerate edge sampling (#1151) · 162dc19a

Da Zheng authored Dec 31, 2019



* accel edge sampling.

* measure sampling time.

* attach positive.

* add neg_deg_sample.

* fix a minor bug.

* remove unnecessary code.

* Revert "add neg_deg_sample."

This reverts commit 45f3c08c87e33589563ca7e6a3ec91cb1239910e.

* Revert "attach positive."

This reverts commit 503d7821555b69b7ccfed55ce8b87ee24fff852d.
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

162dc19a

29 Dec, 2019 1 commit
- [KG] reduce memory consumption. (#902) · f8184153
  Da Zheng authored Dec 28, 2019
```
* reduce memory consumption.

* fix a bug.

* fix a bug.

* fix.
```
  f8184153
24 Dec, 2019 1 commit

[Feature Improvement]Edge Sampler w and w/o replacement (#1116) · 41f8a162

xiang song(charlie.song) authored Dec 24, 2019



* Add weight based edge sampler

* Can run, edge weight work.
TODO: test node weight

* Fix node weight sample

* Fix y

* Update doc

* Fix syntex

* Fix

* Fix GPU test for sampler

* Fix test

* Fix

* Refactor EdgeSampler to act as class object not function that it
can record its own private states.

* clean

* Fix

* Fix

* Fix run bug on kg app

* update

* update test

* test

* Simply python API and fix some C code

* Fix

* Fix

* Fix syntex

* Fix

* Update API description

* add replacement for edge sampler

* Now edge sampler support replacement and no-replacement

* Fix

* Fix

* change kg/app to use edge sampler with replacement config

* Update replacement algo

* Fix syntax

* Update

* Update
Co-authored-by: Da Zheng <zhengda1936@gmail.com>

41f8a162

20 Dec, 2019 1 commit

[Backend] TF backend (#978) · d30a69bf

VoVAllen authored Dec 20, 2019

* tf

* add builtin support

* fiix

* pytest

* fix

* fix

* fix some bugs

* fix selecting

* fix todo

* fix test

* fix test fail in tf

* fix

* fix

* fix gather row

* fix gather row

* log backend

* fix gather row

* fix gather row

* fix for pytorch

* fix

* fix

* fix

* fix

* fix

* fix tests

* fix

* fix

* fix

* fix

* fix

* fix

* fix convert

* fix

* fix

* fix

* fix inplace

* add alignment setting

* add debug option

* Revert "add alignment setting"

This reverts commit ec63fb3506ea84fff7d447a1fbdfd1d5d1fb6110.

* tf ci

* fix lint

* fix lint

* add tfdlpack

* fix type

* add env

* fix backend

* fix

* fix tests

* remove one_hot

* remove comment

* remove comment

* fix

* use pip to install all

* fix test

* fix base

* fix

* fix

* add skip

* upgrade cmake

* change version

* change ci

* fix

* fix

* fix

* fix

* fix seg fault

* fix

* fix python version

* fix

* try fix

* fix

* fix

* tf takes longer time in ci

* change py version

* fix

* fix

* fix oom

* change kg env

* change kg env

* 啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊

* 我再也不搞各种乱七八糟环境了……

* use pytest

* Chang image

d30a69bf